Rapid Multiphase Flow Dynamics Mapped by Single‐Shot MRI Velocimetry

A new, fast magnetic resonance imaging (MRI) method is described and applied to map flow fields in systems with internal velocities rapidly varying along the streamlines. While conventional MRI techniques encode the velocity information in a preparatory period prior to the imaging acquisition module, our technique repeatedly refreshes the velocity encoding during a single‐shot imaging sequence. In this way, the maximum acceleration responsible for velocity variation of the molecules is increased by up to two orders of magnitude compared to standard procedures. Besides being compatible with high acceleration, this pulse sequence is suited to acquiring in a single scan the multiple velocity images required to construct a full velocity vector map. The power of this new methodology is demonstrated by following the internal dynamics of toluene droplets levitating in a counterflow of water during mass transfer of acetone from the water phase into the drop in the presence of surface‐active impurities. The dramatic reduction in measurement time allows visualization for the first time of the important impact of even small concentrations of acetone on accumulation of surfactants at the drop’s surface.     

Correlation between Dynamic Heterogeneity and Local Structure in a Room‐Temperature Ionic Liquid: A Molecular Dynamics Study of [bmim][PF6]

The complex dynamics of a room‐temperature ionic liquid, 1‐n‐butyl‐3‐methylimidazolium hexafluorophosphate ([bmim][PF₆]), is studied using equilibrium classical molecular dynamics simulations in the temperature range of 250–450 K. The activation energies for the self‐diffusion of ions are around 30–34 kJ mol^?1, with that of the anion a little higher than that for the cation. The electrical conductivity of the liquid is calculated and good agreement with experiments is obtained. Structural relaxation is studied through the decay of coherent (total density–density correlation) and incoherent (self part of density–density correlation) intermediate scattering functions over a range of temperatures and wave vectors relevant to the system. The relaxation data are used to identify and characterize two processes, α and β. The dependence of the two relaxation times on temperature and wave vector is obtained. The dynamical heterogeneity of the ions determined through the non‐Gaussian parameter indicates the motion of the cation to be more heterogeneous than that of the anion. The faster ones among the cations are coordinated to faster anions, while slower cations are surrounded predominantly by slower anions. Thus, the dynamical heterogeneity in this ionic liquid is shown to have structural signatures.     

DNA Structural Changes Under Different Stretching Methods Studied By Molecular Dynamics Simulations

We present a molecular dynamics simulation study of 22‐mer DNA conformational variations obtained by stretching both 3′‐termini and both 5′‐termini. Stretching 3′‐termini by 3.5 nm required 142 kJ mol^?1 and the force plateau was ～80 pN, whereas stretching 5′‐termini by the same length required 190 kJ mol^?1 and the force plateau was ～100 pN. Stretching 3′‐termini led to a larger untwisting of the double helix and the successive base pairs rolled to the side of the DNA minor groove, while stretching 5′‐termini resulted in the base pairs rolling to the major groove side and reducing of the diameter of DNA molecule. The most distinctive difference between stretching 3′‐termini and 5′‐termini was that at the force plateau region stretching the 5′‐termini resulted in breakage of the base pairs, which considerably disturbed the structure of the DNA double helix. All of the variations of base rotation and translation for both stretching methods took place when the relative length of DNA l was longer than 1.2, which was the point the force plateau appeared.     

The Conformations of Amino Acids on a Gold(111) Surface

The interactions of amino acids with inorganic surfaces are of interest for biologists and biotechnologists alike. However, the structural determinants of peptide–surface interactions have remained elusive, but are important for a structural understanding of the interactions of biomolecules with gold surfaces. Molecular dynamics simulations are a tool to analyze structures of amino acids on surfaces. However, such an approach is challenging due to lacking parameterization for many surfaces and the polarizability of metal surfaces. Herein, we report DFT calculations of amino acid fragments in vacuo and molecular dynamics simulations of the interaction of all amino acids with a gold(111) surface in explicit solvent, using the recently introduced polarizable gold force field GolP. We describe preferred orientations of the amino acids on the metal surface. We find that all amino acids preferably interact with the gold surface at least partially with their backbone, underlining an unfolding propensity of gold surfaces.     

Local Disorder in Hydrogen Storage Compounds: The Case of Lithium Amide/Imide

Amides and imides of alkali metals are a very promising class of materials for use as a hydrogen‐storage system, as they are able to store and release hydrogen via a chemical route at controllable temperatures and pressures. We critically revise the present picture of the atomic structure of the lightest member (LiNH₂/Li₂NH) by using a combined computational and experimental approach. Specifically, ab initio path integral molecular dynamics simulations and solid‐state ¹H NMR techniques are combined. The results show that the presently assumed local structure might be inconsistent or at least incomplete and needs considerable revision. In particular, the Li atoms turn out to be more mobile and more disordered than suggested by structural data obtained from X‐ray scattering. Also, the configuration of the hydrogen atoms, which is accessible via the NMR experiment and the corresponding first‐principles calculations, is different from the previously assumed data. The computed and experimentally observed ¹H NMR parameters are in very good mutual agreement and illustrate the unusual chemical environment of the hydrogen atoms in this system. Incorporating our results on the new lithium data, we show that the effect of nuclear quantum delocalization for the hydrogen atoms is considerably reduced compared to the perfect crystal structure.     

稀醋酸/水溶液中单个醋酸与水分子的氢键结构

在醋酸/水体系的工业分离中,溶液中的氢键对分离效率有很大影响.本文采用两种第一性原理方法,即从头算分子动力学模拟(AIMD)和量子化学计算(QCC),对由单个醋酸和不同水分子所组成聚合体的氢键相互作用进行了研究,采用极化统一模型和自洽反应场模型计算得到了聚合体在水溶液中的热力学数据.从QCC计算的气相和水溶液中的聚合自由能表明六元环在两种状态下都为最优结构,热力学数据反映出的各种结构的相对稳定性与AIMD模拟的环分布符合得相当一致.研究表明,由于存在醋酸和水分子间的氢键作用,稀醋酸/水溶液中的醋酸分离要比在浓醋酸溶液中困难得多.     

二甲基精氨酸二甲胺水解酶-1的理论研究

运用分子对接和分子动力学方法研究二甲基精氨酸二甲胺水解酶-1(DDAH-1)与其抑制剂亚胺基烯丁基-L-鸟氨酸(L-VNIO)和亚胺基丙基-L-鸟氨酸(Me-L-NIO)的相互作用和结合模式,并根据实验得到的结论设计了亚胺基苯乙基-L-鸟氨酸(Ph-L-NIO)抑制剂.结果表明:L-VNIO比Me-L-NIO对DDAH-1的抑制效果更强,这个结果与实验测得L-VNIO和Me-L-NIO对DDAH-1的半抑制浓度IC50值大小一致.Phe75、Asp78、His172、Ser175和Asp268这五个氨基酸残基在三种抑制剂形成的复合物中起到非常重要的作用,从计算结果推断在这三个抑制剂中我们设计得到的Ph-L-NIO对DDAH-1的抑制效果最好.     

An N log N approximation based on the natural organization of biomolecules for speeding up the computation of long range interactions

Presented here is a method, the hierarchical charge partitioning (HCP) approximation, for speeding up computation of pairwise electrostatic interactions in biomolecular systems. The approximation is based on multiple levels of natural partitioning of biomolecular structures into a hierarchical set of its constituent structural components. The charge distribution in each component is systematically approximated by a small number of point charges, which, for the highest level component, are much fewer than the number of atoms in the component. For short distances from the point of interest, the HCP uses the full set of atomic charges available. For long‐distance interactions, the approximate charge distributions with smaller sets of charges are used instead. For a structure consisting of N charges, the computational cost of computing the pairwise interactions via the HCP scales as O(N log N), under assumptions about the structural organization of biomolecular structures generally consistent with reality. A proof‐of‐concept implementation of the HCP shows that for large structures it can lead to speed‐up factors of up to several orders of magnitude relative to the exact pairwise O(N²) all‐atom computation used as a reference. For structures with more than 2000–3000 atoms the relative accuracy of the HCP (relative root‐mean‐square force error per atom), approaches the accuracy of the particle mesh Ewald (PME) method with parameter settings typical for biomolecular simulations. When averaged over a set of 600 representative biomolecular structures, the relative accuracies of the two methods are roughly equal. The HCP is also significantly more accurate than the spherical cutoff method. The HCP has been implemented in the freely available nucleic acids builder (NAB) molecular dynamics (MD) package in Amber tools. A 10 ns simulation of a small protein indicates that the HCP based MD simulation is stable, and that it can be faster than the spherical cutoff method. A critical benefit of the HCP approximation is that it is algorithmically very simple, and unlike the PME, the HCP is straightforward to use with implicit solvent models. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010